Mercurial > repos > iuc > mothur_heatmap_bin

diff heatmap.bin.xml @ 1:70cd6357502a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:14:00 -0400
parents 712b61562375
children 1cc0526b5a0f
line wrap: on
line diff
--- a/heatmap.bin.xml	Fri Jun 24 16:35:19 2016 -0400
+++ b/heatmap.bin.xml	Fri May 19 04:14:00 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$input.otu" input_otu.dat &&
 
@@ -34,6 +37,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -118,13 +122,13 @@
 @MOTHUR_OVERVIEW@
 
 
-**Command Documenation**
+**Command Documentation**
 
 The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin
+.. _list: https://www.mothur.org/wiki/List_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
 
 v.1.21.0: Updated to Mothur 1.33
 ]]>